NU32CH10-Jones ARI 9 July 2012 19:2

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Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]
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Dean P. Jones, Youngja Park, and Thomas R. Ziegler

Department of Medicine, Emory University, Atlanta, Georgia 30322;
email: dpjones@[Link], [Link]@[Link], tzieg01@[Link]

Annu. Rev. Nutr. 2012. 32:183–202 Keywords

First published online as a Review in Advance on systems biology, microbiome, prevention, mass spectrometry,
April 23, 2012
personalized medicine, exposome
The Annual Review of Nutrition is online at
[Link] Abstract
This article’s doi: Nutritional metabolomics is rapidly maturing to use small-molecule
10.1146/annurev-nutr-072610-145159
chemical profiling to support integration of diet and nutrition in com-
Copyright  c 2012 by Annual Reviews. plex biosystems research. These developments are critical to facilitate
All rights reserved
transition of nutritional sciences from population-based to individual-
0199-9885/12/0821-0183$20.00 based criteria for nutritional research, assessment, and management.
This review addresses progress in making these approaches manageable
for nutrition research. Important concept developments concerning the
exposome, predictive health, and complex pathobiology serve to empha-
size the central role of diet and nutrition in integrated biosystems models
of health and disease. Improved analytic tools and databases for tar-
geted and nontargeted metabolic profiling, along with bioinformatics,
pathway mapping, and computational modeling, are now used for nutri-
tion research on diet, metabolism, microbiome, and health associations.
These new developments enable metabolome-wide association stud-
ies (MWAS) and provide a foundation for nutritional metabolomics,
along with genomics, epigenomics, and health phenotyping, to sup-
port the integrated models required for personalized diet and nutrition
forecasting.

183
 NU32CH10-Jones ARI 9 July 2012 19:2

substantial simplification and many as-

Contents sumptions. Despite this, modern nutrition has
provided a manageable system for nutrition sci-
INTRODUCTION . . . . . . . . . . . . . . . . . . 184
entists to understand the mechanistic basis for
CONCEPTUAL DEVELOPMENTS 185
requirements and clinical nutritionists and di-
The Exposome and Nutritional
etitians to develop dietary and nutritional plans
Metabolomics . . . . . . . . . . . . . . . . . . 186
to minimize and remediate nutrition-related
Predictive Health and Healthcare
disease. This was achieved using a central as-
Economics . . . . . . . . . . . . . . . . . . . . . 188
sumption that health and disease among popu-
Nutritional Metabolomics for
lations and in individuals may be determined by
Complex Biosystems Research . . . 189
variations of the same biochemical system with
PROFILING METABOLITES FOR
common biochemical requirements. To a first
NUTRITIONAL
approximation, this assumption is true; nor-
METABOLOMICS . . . . . . . . . . . . . . . 190
mative descriptions, such as Dietary Reference
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

Mass Spectrometry . . . . . . . . . . . . . . . . . 191

Intake (DRI) values, accurately describe the
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High-Resolution Mass
collective needs of individuals; DRIs along with
Spectrometry . . . . . . . . . . . . . . . . . . . 191
food guides are useful to promote health and re-
Other Analytic Approaches . . . . . . . . . 192
duce disease collectively for individuals within
BIOINFORMATICS AND
the population. From the standpoint of public
COMPUTATIONAL
health, this approach is effective and successful.
SCIENCES . . . . . . . . . . . . . . . . . . . . . . . 192
During the past decade, many distinguished
Database Tools . . . . . . . . . . . . . . . . . . . . 193
scientists have emphasized (26–29, 79, 98, 101,
Top-Down Approaches
107) that new technologies in metabolomics,
Complement Bottom-Up
along with genomics, epigenomics, transcrip-
Metabolomics . . . . . . . . . . . . . . . . . . 194
tomics, and proteomics, enable approaches that
Bioinformatics for Top-Down
have the potential to expand this effective public
Metabolomics . . . . . . . . . . . . . . . . . . 195
health strategy with an improved approach for
Artificial Intelligence: Fractal
personalized nutrition, i.e., to address nutrition
Analysis . . . . . . . . . . . . . . . . . . . . . . . . 196
at n = 1. The full implications of this are only
CONCLUSIONS AND NEW
beginning to be discussed; the transition may
PERSPECTIVES . . . . . . . . . . . . . . . . . 196
not be incremental improvements of current
nutritional science, such as having better ways
to study pathways of iron metabolism or more
precise ways to measure phytochemicals in
INTRODUCTION green tea. Instead, personalized nutrition
Each person has a unique genome and is an in the future may require a considerable
ongoing nutritional experiment from concep- expansion of the conceptual framework for
tion to death. A large number of functional nutrition science that has emerged over the
redundancies and adaptive mechanisms serve past century. Diet and nutrition are inherently
to provide homeostasis despite a considerable complex: Hundreds of foods are derived
range of developmental, dietary, infectious, and from heterogeneous plant- and animal-based
Normative: other environmental challenges. Differences in nutrients and nutrient substrates; food storage,
description of
nutrient intake cause epigenomic changes (10, processing, and preparation methods vary;
characteristics and
responses in terms of 56) so that an n = 1 nutritional experiment may consumption, digestion, and absorption are
population averages not be reproducible even within the context of heterogeneous over the lifespan within individ-
DRI: Dietary an individual over time. Application of scien- uals; specific nutrients, such as zinc or vitamin
Reference Intakes tific method to define nutritional requirements D, impact hundreds of molecular systems;
relevant to an individual therefore requires molecular systems are highly regulated and

184 Jones · ·
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 NU32CH10-Jones ARI 9 July 2012 19:2

adaptive. To date, the framework in nutrition on disease (76). The present review is focused
science has been largely reductionist in nature on recent progress in making nutritional
(e.g., by focusing on deviations from the norm, metabolomics tractable for nutritional scien-
Reductionist:
one nutrient at a time). Examples include tists to transform nutritional evaluation and description of complex
single nutrition deficiencies or excesses, and management from a normative, population- system behavior in
single gene variants (with variable penetrance), based approach to one utilizing individual char- terms of simple cause-
that are useful to predict clinical responses acteristics in an integrated, complex systems effect relationships
in homogeneous groups of individuals. approach. Progress is ongoing in many scien- Nutritional
However, emerging technologies including tific disciplines that are peripheral to nutrition metabolomics:
use of small-molecule
metabolomics approaches now allow investi- but central to integrated systems biology (89,
chemical profiling to
gation of the complexity of interactions of all 91). By necessity, we only briefly summarize integrate diet and
of the nutrients within a complex individual these, focusing on conceptual developments nutrition in complex
having a unique genome and history of dietary, in integrative biology, analytic methods that biosystems
environmental, and behavioral exposures. support hybrid approaches for targeted (e.g., in Exposome: life-
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

In this review, we define nutritional identification of potential direct or surrogate course environmental
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metabolomics as the use of small-molecule biomarkers of health, disease, and mechanistic exposures (including
lifestyle factors) from
chemical profiling to integrate diet and nu- pathways) and nontargeted metabolic pro-
the prenatal period
trition in complex biosystems. This explicitly filing, and bioinformatic and computational onward
defines nutritional metabolomics as an experi- approaches to facilitate interpretation and use
Predictive health:
mental approach that uses chemical profiling in of complex data. Although routine use of such a healthcare concept
a global manner, i.e., as a component of a com- approaches in applied nutrition must await using lifestyle
plex systems approach to diet and health. With development and testing prior to implementa- approaches, including
this definition, profiling of chemicals, whether tion, an extensive array of metabolic profiling nutrition, to optimize
vitality and well-being
targeted or nontargeted, is necessary but insuf- and computational capabilities is now available
rather than to serve
ficient for the transformation to personalized to support basic research to enable this tran- primarily as a means to
nutrition. Progress in nutritional metabolomics sition. Progress in these areas suggests that prevent disease
is measured by steps to support facile use of nutritional metabolomics has advanced toward
chemical profiles to enhance practice at the establishing a critical foundation to define the
level of an individual. For instance, a manage- cumulative dietary and nutritional exposures
able system for an average practitioner may be of an individual impacting personal health.
a series of nutrition forecasting models, much
like weather forecasting systems used to pre-
dict the occurrence, paths, time course, and
severity of hurricanes. Such nutritional mod- CONCEPTUAL DEVELOPMENTS
els would use metabolic profiles along with Three important conceptual developments
genomic, epigenomic, and health phenotyping have occurred during recent years that impact
to predict health outcomes and relevant time the transition from targeted nutritional bio-
frames from dietary and nutritional practices. chemical studies describing population aver-
The practitioner of the future will evaluate re- ages to nutritional metabolomics studies de-
sults of computer-based models and develop in- scribing personalized nutritional needs. These
terventional plans based upon these results. include the concept of (a) the exposome, in
Many reviews and commentaries address which cumulative exposures throughout life
the challenges and limitations in application are incorporated into models of health (100);
of metabolomics to nutrition, diet, and health (b) predictive health, in which nutritional guid-
(26–29, 79, 98, 101, 107). Much of this has been ance to prevent disease is replaced by nutrition
focused on the use of nutritional metabolomics designed to optimize vitality and well-being
to discover new biomarkers of nutritional expo- (60); and (c) individual complexity, in which
sure, nutritional status, and nutritional impacts models include multiple interacting functional

[Link] • Nutritional Metabolomics 185

 NU32CH10-Jones ARI 9 July 2012 19:2

networks rather than unrealistic reductionist study of the effects of undernutrition and
cause-effect models (17). overnutrition for each of the required nutrients
on the core nutritional metabolome under
KEGG: Kyoto
Encyclopedia of Genes controlled conditions is feasible with current
The Exposome and Nutritional technologies. Such studies are central to a
and Genomes
Metabolomics conceptual grid for the exposome created
MMCD: Madison
Metabolomics Christopher Wild introduced a bold and vision- by combining exposures of the life cycle
Consortium Database ary concept in 2005 advocating the need for re- (Figure 1b) with the exposures contributing to
Pan-metabolome: search to define exposures that complement the the pan-metabolome (Figure 1a).
all small-molecular- genome in defining health risks (100). He used Most chemicals in food are not nutrients
weight chemicals in a the term “exposome” to encompass life-course (Figure 1a). Some phytochemicals are biolog-
biologic system
environmental exposures (including lifestyle ically active and important to health, such as
factors), from the prenatal period onward, and inducers of detoxification systems that protect
proposed the development of a conceptual against cancer-causing reactive electrophiles
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

grid for exposure research to complement the (52) and antioxidants that protect against dam-
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Human Genome Project. While relevant for age from free radical reactions (24). However,
environmental science (75), this also provides these phytochemicals are highly variable within
a basis for systematic integration of life-cycle individual food sources and thus in the diet,
research. Varying nutritional needs during the and the complexity of diet and overlapping
life cycle are central to nutritional sciences biologic activities of chemicals has prevented
and provide a foundation for public health clear understanding of their importance, as ev-
policy (59, 69). Thus, application of nutritional idenced by the failure of interventional trials
metabolomics to improved life-cycle nutrition based upon extensive experimental and obser-
research can yield a central foundation to oper- vational research (34, 46). Goodacre et al. (33)
ationalize the conceptual grid of the exposome estimated that there are more than 200,000
(Figure 1). metabolites within the plant kingdom, and new
Web-based tools to facilitate research on plant
Food metabolome. In the exposome, diet is metabolomics have become available (3, 67).
probably the greatest single source of chemical Advances relevant to nutritional metabolomics
exposures, including nutrients, nonnutritive have been made in food and agricultural sci-
chemicals, pesticides, and others. About 40 ences (16, 37). Even though the primary pur-
required nutrients are consumed daily in poses are not nutrition per se, the use of chem-
variable amounts by individuals. Among ical profiling as a basis to characterize plants
these, the organic chemicals are converted and plant-derived products is of great impor-
through intermediary metabolism to more tance to support detailed nutritional interven-
than 1,500 chemicals, which are now included tion and epidemiology studies. For instance,
in curated databases such as the Kyoto En- characterization of chemicals in grapes and
cyclopedia of Genes and Genomes (KEGG) products such as wine provide an important
human metabolic pathways (48, 49), Madison subset of dietary chemicals that are relevant to
Metabolomics Consortium Database (MMCD) diet and health (25, 77). Common and abun-
(60), and Metlin database (82). Lipidomics dant phytochemicals are already included in hu-
research shows that the full spectrum of en- man metabolomics databases, such as KEGG,
dogenous metabolites is much larger, perhaps Metlin, and MMCD, and are readily accessi-
hundreds of thousands of chemical species ble to nutrition scientists. Other chemicals are
(39). These nutrients and related products included in more specialized resources (23, 30,
can be considered operationally as a core 53), some with open access and others that are
nutritional metabolome, which contributes to proprietary. The task of learning the tools and
the pan-metabolome (Figure 1a). Systematic their respective strengths and weaknesses for

186 Jones · ·
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 NU32CH10-Jones ARI 9 July 2012 19:2

nutrition research remains challenging because of diet-derived phosphatidylcholine (choline,

food and nutrition are inherently complex and trimethylamine N-oxide, and betaine) predict
there are many databases. Critical challenges risk for cardiovascular disease. Wikoff et al. (99)
Microbiome:
remain to link crop metabolomics (81) with used a mass spectrometry approach to study the microorganisms
food metabolomics (food storage, processing, effect of the intestinal microbiome on plasma associated with a
and cooking) (11, 101) and human nutrition. metabolites in germ-free mice compared to metazoan organism
Considerable scientific information is available conventional mice. Of the chemicals found in
concerning loss of nutrient content and forma- both, about 10% significantly differed between
tion of chemical carcinogens, but manual cura- the mice, and hundreds of chemicals were de-
tion of such information into readily accessible tected in only one group. One can infer that
databases is costly and time-consuming. Addi- greater than 10% of the plasma metabolome
tionally, characterization of chemicals formed is directly dependent upon the microbiome.
during storage and handling is mostly limited to Specific studies showed that bacteria produced
highly toxic metabolites and degradation prod- indole-containing metabolites derived from
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

ucts. Thus, an alternative approach would be tryptophan such as indoxyl sulfate and indole-3-
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to use the advances in analytic methods for nu- propionic acid (99). Together, these results il-
tritional metabolomics to create an integrated lustrate significant interplay between bacterial
pipeline for this complex subject, fostering the and mammalian metabolism both at the level
critical links between plant science, food sci- of macronutrition and at the level of specific
ence, and human nutrition needed for complex metabolic pathways linked to disease.
systems models of diet and health (79).
Environmental metabolome. The food
Microbiome-related metabolome. Impor- metabolome also contains herbicides, insec-
tant advances have come from the recog- ticides, fungicides, and other chemicals of
nition of the contribution of the enteric interest for environmental health (Figure 1a).
microbiome to the mammalian metabolome Although not a central component of nutri-
(Figure 1a). Martin et al. (63) used a top- tional metabolomics research per se, these are
down metabolomics approach, i.e., one ex- relevant because environmental chemicals are
amining all chemicals detected rather than present to variable extents in all metabolomics
only a targeted subset, to study the inter- studies, and nutrient-chemical interactions
action of symbiotic gut microorganisms with could represent a common determinant of
mouse metabolism. Comparisons of germ-free environmental health. High-performance
mice colonized by a human baby flora or a metabolic profiling of human plasma revealed
normal flora to conventional mice showed a over 100 chemicals apparently of environ-
simple microbiome/metabolome correlation mental origin (84). Such environmental
network, impacting directly on the host’s abil- chemicals, as well as other chemicals derived
ity to metabolize lipids. They concluded that from commercial products (face creams, soaps,
the microbiome modulates absorption, storage, disinfectants, flame retardants, etc.) and con-
and energy harvest from the diet at the systems taminants in the drinking water (antibiotics,
level. Associations between early nutrition, the fertilizers, drugs, etc.), can potentially interact
microbiota, and the immune system are be- with nutrients to impact health. Environmental
ing actively studied as contributors to obesity contaminants are present in all of the solvents
and chronic disease (19, 65). Wang et al. (95) and materials used for collection and analysis
used liquid chromatography-mass spectrome- of samples, and precautions and controls for
try and a combination of human and mouse proper interpretation have been developed
studies to generate unbiased small-molecule (1, 51). Thus, progress in environmental
metabolic profiles of plasma. They found metabolomics provides information critical
that three microbiome-dependent metabolites to the elaboration and development of the

[Link] • Nutritional Metabolomics 187

 NU32CH10-Jones ARI 9 July 2012 19:2

exposome and, ultimately, to effectively utilize transition of medicine from a disease-oriented

nutritional metabolomics for the study of model to a health-oriented model.
complex interactions that impact personalized
Integrated
biosystems: models nutrition. Normative approach. In this vision, contem-
incorporating porary nutrition uses a normative approach
functional (Figure 2a) in which average characteristics in
relationships of populations and model systems support the de-
component parts to Predictive Health and velopment of hypotheses, which are then tested
describe overall Healthcare Economics
behavior of a in human studies to determine the average re-
biological system Nutritional and dietary recommendations sponse of a selected population to an interven-
are focused on disease prevention and man- tion. Prevention and treatment plans then use
agement, codified as a set of reference values this treatment for an individual who meets the
(DRI) that is defined as the amounts of essential selection criteria, i.e., deviates from “normal,”
nutrients considered sufficient to meet the with the expectation that the treatment that
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

physiologic needs of practically all healthy showed significant benefit in the test popula-
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persons in a specified group and the average tion will be beneficial in the individual.
amount of food sources of energy needed by the
members of the group (58). While maintaining Integrated biosystems approach. An inte-
a focus on healthy people, a shift has occurred grated biosystems approach (Figure 2b) also
in recent years to include recommendations uses information from population and molec-
concerning nonnutritive food components, ular studies as above, but this information is
such as fiber, and also to include recommen- used as a basis for design of integrated systems
dations for overweight people to promote models that predict behavior (90). Computa-
health (88). Although gradual, this shift from tional models based upon these integrated de-
a focus on sufficient nutrition to avoid disease signs can then be used to evaluate effects of
to a focus on nutrition to optimize overall varying single or multiple elements within the
health and function is fundamental. It redirects model, as is needed to predict outcome for an
nutrition sciences from individual nutrients to individual with a unique set of characteristics.
eliminate specific disease symptoms to opti- As models are refined and validated with in-
mized balances for healthy physical, mental, clusion of information-rich data, such as nutri-
and emotional development. This advanced tional metabolomics, they can be used for per-
concept sets the stage for evolution of complex sonalized health prediction, risk evaluation, and
systems models for personalized nutrition. treatment. This is advantageous in the transi-
Concept development was advanced in a tion from an average (population) model be-
commentary on predictive health and person- cause it can be individualized as much as the
alized medicine (90) in which the authors em- data will allow.
phasized that establishing “personalized health Implementation of integrated systems
profiles” will be a challenging task that is de- models in healthcare will face many regulatory
pendent upon integrated systems approaches. hurdles, and the cost of surmounting these
They suggest that the required shift in think- barriers limits incremental improvements.
ing by scientists and practitioners will be a Thus, even though gradual improvement
greater challenge than to create mathemat- would appear possible, substantially improved
ical models of complex diseases. They pre- personalized models are needed to warrant the
dict, however, that this shift will ultimately oc- cost of validation studies. The development
cur because of the cost of the current model of highly precise personalized models is not
of healthcare. Progress in conceptualizing this likely to be straightforward, and there is a
shift for nutritional sciences is summarized possibility that the interactions of the genome,
in Figure 2, based upon this vision for the epigenome, and diet and health behaviors

188 Jones · ·
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 NU32CH10-Jones ARI 9 July 2012 19:2

are so complex that useful integrated systems medicine, based upon observed associations be-
models will not become available for decades. tween nutrient intake and clinical syndromes,
with supportive mechanistic studies to link nu-
Artificial
Artificial intelligence approach. An alter- trients to phenotypes. In practice, effectiveness intelligence: use of
native (Figure 2c) is to use systems data and of contemporary nutrition depends upon ob- machine learning for
associated detailed health outcomes data with servational skills of a nutritionist and relatively classification or
artificial intelligence. For this, data for a large simple assessment and intervention tools. Al- decision-making
purposes without
reference population would be assembled into though effective, the approach has limitations
regard for underlying
a cumulative data matrix so that data for an in sensitivity to detect early or subclinical nu- mechanisms or
individual can be queried against the matrix tritional insufficiencies, accuracy for different relationships of
to obtain the best matches to directly predict clinical presentations, and usefulness in thera- component parts
outcomes. Although less attractive from a peutic interventions for complex phenotypes.
scientific point of view, this may be more effec- A greater limitation to contemporary
tive in rapidly providing personal predictions approaches, however, is that rational interpre-
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

for human nutrition because of the extensive tations based upon a system that excessively
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variability of human diet, individual genet- relies upon reductionism can be mostly or
ics, etc. An advantage of this approach is that completely wrong. Loscalzo et al. (57) used
the power of prediction would increase with the the failure of secondary interventional trials
number of individuals in the database and the with folate to reduce risk of atherothrombotic
period of time over which data are collected. events with vascular disease and hyperhomo-
Progress with virtual clinical data warehouses cysteinemia to illustrate the limitations of this
(14, 97) and information systems (36, 106) approach. They used sickle cell disease, in
provides capabilities to use metabolomics data which a single DNA mutation can have multiple
to support this approach to personalized nutri- disease phenotypes, as a second example (57).
tion. Although there are many practical issues Other examples are common: Cardiovascular
concerning policy and implementation of such disease has multiple nutrition-related compo-
new approaches, the conceptual development nents, including high low-density lipoprotein,
has advanced to enable nutrition scientists to low high-density lipoprotein, uncontrolled
effectively use nutritional metabolomics toward hypertension, physical inactivity, smoking,
the long-term goal of improved individual obesity, and uncontrolled diabetes, but none of
nutritional assessment, health prediction, and these is perfect in prediction; phenylketonuria
therapeutic intervention. has multiple phenotypic characteristics that
are not uniformly expressed; many diseases
have genetic and nongenetic bases. Nutritional
Nutritional Metabolomics for metabolomics studies reinforce the conclusion
Complex Biosystems Research that average population characteristics are not
A third conceptual advance lies in the transition good descriptors of individual characteris-
from simple cause-effect models of disease to tics. In a diurnal variation study, an average
ones acknowledging that in complex, adaptive variation in the plasma metabolic profile was
systems, a single cause can have multiple identified that discriminated morning, evening,
effects, and multiple causes can have a single and nighttime metabolic patterns (71). No
effect. Loscalzo et al. (57) addressed the chal- individual had the average response pattern;
lenging transition from contemporary medical i.e., even though an average response was de-
classification of human disease, derived from scribed, this average was not a good descriptor
conventional reductionism, to one that incor- of an individual. A crossover study of sulfur
porates a nonreductionist approach to systems amino acid insufficiency similarly showed that
biomedicine. Contemporary nutrition was although about half of the individuals showed
derived in a manner similar to contemporary a common response pattern, no individual

[Link] • Nutritional Metabolomics 189

 NU32CH10-Jones ARI 9 July 2012 19:2

had an average response pattern (72). Thus, biochemical reactions occur in different sub-
nutritional metabolomic data underscore cellular compartments linked by transport sys-
the need to transition to complex biosys- tems (Figure 3). In such multidimensional
tems approaches to transform nutrition to a models, movement between compartments can
personalized level. compensate for changes within compartments.
A study by Deo et al. (15) illustrates Because volumes, concentrations, and enzyme
the important contribution of nutritional contents of compartments differ, the response
metabolomics toward the goal of complex of a complex system is often not a sim-
biosystems models. Nutritional science with an ple function. Similarly, differences in gene
n = 1 is practiced daily with conduct of glucose copy number, alleles, gene expression, epige-
tolerance tests. Insulin affects many processes nomic regulation, microRNAs, cell popula-
in addition to blood glucose levels, and glucose tions, and a number of other mechanisms con-
availability impacts many aspects of metabolism tribute to the multidimensional character of
in different body compartments. Deo et al. (15) complex systems. Hence, the use of nutri-
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

showed that considerable additional informa- tional metabolomics in integrated biosystems

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tion about an individual could be obtained by research represents a critical advance in ad-
applying nutritional metabolomics methods in dressing complex issues of diet and health.
association with a challenge test. They analyzed
results of targeted metabolic profiling in asso-
ciation with an oral glucose tolerance test and PROFILING METABOLITES FOR
found few chemicals corresponding to those ex- NUTRITIONAL METABOLOMICS
pected from known metabolic pathway metabo- The small-molecular-weight metabolites
lites in comparison of normal glucose tolerance within an organism cannot all be measured
with impaired glucose tolerance. However, us- due to the practical limit of sensitivity, i.e.,
ing unbiased approaches with bioinformatics detection methods are inadequate to mea-
tools, active modules of metabolites were iden- sure all individual small molecules. Human
tified that were naturally grouped according to metabolic databases include approximately
system A and system L amino acid transporters 2,500 metabolic intermediates, hormones,
and the osmolyte transporter SLC6A12 (15). and other signaling molecules, over 1,000
Additional contribution by the mitochondrial drugs, and over 3,500 food components (60,
glutamate-aspartate transporter SLC25A13 82, 102). Many analytic methods are available
was indicated by changes associated with pyrim- to acquire extensive metabolic information,
idine biosynthesis (OMP, ribose-1-phosphate), and the strengths and weaknesses of these
purine biosynthesis (ribose-1-phosphate, xan- have been recently reviewed (40). No single
thine, hypoxanthine, xanthosine), triglyceride method has achieved a level of standardization
biosynthesis (glycerol, glycerol-3-phosphate), or widespread use to warrant consideration as a
urea cycle (citrulline, ornithine), bile salt uniform platform for nutritional metabolomics.
accumulation (taurochenodeoxycholate, gly- Although thousands of chemicals can be mea-
cocholate, glycochenodeoxycholate), glycoly- sured by current technologies, it is humbling
sis (lactate, pyruvate), gluconeogenesis (ala, to recognize that today’s analytic platforms for
ser), malate shuttling (glutamate, malate, targeted measurement of biochemicals cannot
alpha-ketoglutarate) and aspartate biosynthe- quantify more than 10 times the number of
sis (asparagine). The data illustrate an im- chemicals measured by Moore and colleagues
portant conceptual advance in nutritional half a century ago using automated amino acid
metabolomics, namely, transitioning from a analysis (64). Nutrition research favors rigor-
mono-dimensional view of metabolism involv- ous analytic procedures in which individual
ing only substrate clearance or enzymatic con- analytes are quantified in absolute amounts
versions to a multidimensional view in which relative to authentic standards. In amino acid

190 Jones · ·
Park Ziegler
 NU32CH10-Jones ARI 9 July 2012 19:2

analysis, the amine moiety allowed chemical support separation of thousands of chemicals
modification and quantification in terms of in relatively short analysis times (96). Absolute
an added molecular tag. Because metabolites quantification by mass spectrometry requires
MS: mass
differ considerably in physical and chemical standardization relative to authentic standards spectrometry
properties, this approach is inherently limited and is often readily achieved only for small
FTMS: Fourier-
to capture the entire metabolome. Conse- numbers of metabolites. The limited ability transform mass
quently, a central challenge remaining for to obtain absolute quantification of large spectrometry
nutritional metabolomics is the development numbers (>2,000) of metabolites remains a apLCMS: adaptive
of comprehensive profiling capabilities. major obstacle for nutritional metabolomics. processing of high-
An important practical advance that makes resolution liquid
metabolic profiling tractable for nutritional sci- chromatography/mass
Mass Spectrometry ences is the availability of the mass spectral
spectrometry data

All molecules have mass, and advanced mass analyses in academic cores and commercially
detectors in mass spectrometry (MS) currently (e.g., Metabolon in Research Triangle Park,
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

provide the best methods to detect the broad North Carolina). Although absolute quantifi-
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range of chemicals. MS detects chemicals as cation is not achieved, relative quantification is

ions in the gas phase, and this presents practical sound for samples collected, stored, and ana-
limitations to obtain absolute quantification lyzed together in sample sets. If one uses the
of a spectrum of chemicals. Chemicals differ 2,500 metabolic intermediates in the Human
considerably in the conditions required for ion- Metabolome Database (102) as a reference,
ization in the gas phase. The energy required to analytic methods are widely available to gain
create ions can result in reactions that convert information on 10% of the metabolites of in-
metabolites to different chemical species. Fur- termediary metabolism for nutrition studies.
thermore, a single chemical can form multiple
ionic forms, and relative amounts of these
forms can vary due to the presence of other High-Resolution Mass Spectrometry
chemicals. These limitations are controlled High-resolution mass spectrometry (62)
by standardized separation techniques (gas has been used to facilitate measurement of
chromatography, liquid chromatography, large numbers of chemicals based upon mass
capillary electrophoresis), which simplify the resolution and mass accuracy (Figure 4).
mixture of chemicals introduced into the mass These characteristics allow prediction of
spectrometer, and ionization methods (elec- elemental composition of a chemical using
trospray ionization, ESI; atmospheric pressure the accurate mass/charge (m/z) values; >90%
chemical ionization, APCI; desorption electro- of the metabolites in the MMCD or KEGG
spray ionization, DESI), which ionize a broad human metabolite databases have unique
range of chemicals (79). Currently, targeted elemental compositions so that m/z matching
analysis of more than 300 known metabolites to the databases provides a fairly effective
in biological samples is widely available, approach to map metabolism. Using this
with reliable relative quantification within approach, a single 10-minute analysis by
sample sets. Gas and liquid chromatography liquid chromatography–Fourier transform
separations are most commonly used, with ion mass spectrometry (LC-FTMS) (84) with
dissociation using tandem mass spectrometry data extraction by adaptive processing of
(MS/MS) to facilitate chemical identifica- high-resolution liquid chromatography/mass
tion. Ongoing improvements in MS/MS spectrometry data (apLCMS) (105) detects
databases (60) (National Institute of Standards; about 4,000 m/z, which include matches to
[Link] about 25% of the metabolites in KEGG
continue to enhance capabilities, and advances human metabolic pathways (Figure 5).
in ultra-high-pressure liquid chromatography Targeted quantification can be obtained by

[Link] • Nutritional Metabolomics 191

 NU32CH10-Jones ARI 9 July 2012 19:2

stable isotope dilution (44, 45) and by con- analysis while simultaneously performing un-
current MS/MS analysis, matched back to targeted testing for other associations among
authentic standards and MS/MS databases. unidentified chemicals.
Greater coverage (about 7,000 m/z) is obtained In summary, progress in the development
with a dual-chromatography–FTMS approach of analytic tools for nutritional metabolomics
(84), and data extraction by apLCMS with has made targeted (biomarker or mechanistic
multiple parameter settings and data merger discovery) and untargeted metabolite analysis
can further increase the number of m/z features practical for routine inclusion into labora-
detected in a single sample. Importantly, the tory, clinical, and epidemiological nutrition
coverage can, in principle, be increased to research. Limitations remain for absolute
detect over 10,000 chemicals, including repre- quantification, but relative quantification of
sentative chemicals of each of the components ≈10% of the core nutritional metabolome
of the pan-metabolome. Such coverage enables of humans is readily available to support
studies similar to genome-wide association integrated studies of diet and health. Non-
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

studies, in which abundance of individual targeted analyses using high-resolution mass

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chemicals are tested for association with spectrometry provide relative quantification
health phenotypes. These metabolome-wide of thousands of chemicals, over half of which
association studies will be very important to are currently unidentified. These include
link dietary chemicals with disease. Related bioactive phytochemicals and products of the
analyses can support metabolome-genome microbiome. Hybrid approaches for targeted
association and metabolome-epigenome as- and untargeted analyses provide information-
sociation studies. Improved classification of rich data sets to enable bioinformatic and
the pan-metabolome as outlined in Figure 1 computational research to address complex
will further allow more specific analyses of the interactions of diet and the microbiome as they
nutritional metabolome and food metabolome. impact individual nutritional needs.

Other Analytic Approaches BIOINFORMATICS AND

Many additional approaches are available for COMPUTATIONAL SCIENCES
nutritional metabolomics, such as capillary Biostatistical, bioinformatic, and computa-
electrophoresis as an alternative to chromatog- tional tools to analyze chemical profiles have
raphy (83) and electrochemical detection as an been developed over several decades and used
alternative to mass spectrometry (55). A com- extensively for nutritional biomarker discov-
mon approach to improve detection of metabo- ery (7). In the past several years, important
lites that differ in characteristics of ionization advances have been made in tools and appli-
or separation is to combine results from multi- cations to use information-rich metabolomics
ple analytic platforms. Innovative approaches data to integrate diet and nutrition in complex
include biosensor arrays, microfluidics, and biosystems. These tools can be used in both
alternate spectral methods, such as Fourier- bottom-up and top-down approaches (4, 45, 63,
transform infrared spectroscopy (13, 54, 108). 75). Bottom-up approaches start with known
An important advance from the commercial molecular reactions and add known steps with
sector (Metabolon in Research Triangle Park, targeted metabolic analyses to create models
North Carolina) is the introduction of a hybrid of complex behavior. Important advances have
approach for metabolomics, consisting of tar- been made in metabolic flux and contribu-
geted analysis of 300 to 500 known chemicals tions of discrete biochemical pathways to com-
and untargeted analysis of an additional 3,000 plex processes. For example, Wopereis et al.
unidentified m/z. This hybrid approach allows (103) studied the effect of an anti-inflammatory
one to test specific hypotheses using targeted drug, diclofenac, on 343 plasma metabolites

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during an oral glucose tolerance test. Metabo- number of Web sites. Software tools for query-
lites that change grouped into patterns, one ing and visualizing metabolic networks support
of which included increases in neutral amino description and prediction of metabolic path-
acids (Ile, Leu, Thr) over the entire challenge ways for a wide variety of organisms and con-
time course and the other including metabo- stitute an important resource for nutrition re-
lites (5-oxoproline, Gly, Glu) related to glu- search. Such developments have occurred as
tathione biosynthesis that were increased only a consequence of genome sequencing efforts
after 90–120 minutes. Diclofenac was found and algorithms for predicting the presence of
to selectively increase the latter group. Wang metabolic pathways in organisms with a se-
et al. (94) studied a panel of >60 amino acids, quenced genome. These are mostly nonquanti-
amine, and other polar metabolites in a case- tative at the present time, but combination with
control study of normoglycemic individuals fol- enzyme databases containing kinetic informa-
lowed over 12 years and found branched-chain tion (35, 80) is beginning to provide more com-
and aromatic amino acids as predictors of fu- prehensive modeling capabilities such as are re-
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

ture diabetes. Isotopic tracer methods in nutri- quired to describe nutrient effects.
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tional metabolomics have also contributed to a As an example, MetaCyc is a database

number of important nutritional requirements of nonredundant, experimentally elucidated
of disease. Marrero et al. (61) used 13 C car- metabolic pathways from >1,000 organisms
bon tracer kinetics to study gluconeogenesis in (mostly microorganisms and plants) that has
Mycobacterium tuberculosis, which relies on this begun to capture enzyme kinetics data. The
metabolic process to establish and maintain in- database includes more than 1,500 metabolic
fection. Beste et al. (6) used tracer studies to pathways and associated 8,600 enzymatic
identify a novel pathway for pyruvate dissim- reactions. Such systems can support computa-
ilation requiring CO2 fixation. Ferrara et al. tional metabolic network prediction, integrate
(22) combined transcriptomic data for 40,000 experimental data into metabolic pathways,
probe sets with targeted analysis of 67 interme- and create metabolic models for simulation
diary metabolites (amino acids, organic acids, (8, 50). An important advance for nutritional
acyl-carnitines) to construct causal networks metabolomics is the development of a comple-
of metabolic processes in liver. Such examples mentary experimental approach to use stable
provide clear evidence of the progress in ap- isotopes to elucidate metabolic pathways in a
plication of bioinformatics and computational nontargeted manner (41). This method uses the
approaches to address complex nutritional isotopomer distribution and computation anal-
questions. ysis for global analysis of flux into all detectable
metabolite pools. Such methods remain limited
by metabolic cycles, loss of label as CO2 , and an
Database Tools assumption that the system is at a steady state.
Developments for the study of specific nutri- Despite these limitations for precise systems
ent effects on metabolism include substantial biology descriptions, however, the methods
advances in biosystems databases. The conflu- provide means to elucidate new metabolic
ence of genome sequencing and bioinformat- pathways and could be especially valuable for
ics has led to the development of thousands studies of nutrition and the microbiome.
of metabolic databases such as the MetaCyc, These database tools support genome-scale
KEGG, Reactome, Model SEED, and BiGG models of metabolism as needed to address the
families (50). These are developed using manual effects of diet and nutrition on health of an
curation of scientific data, often focusing on hu- organism. Although a review of research on
mans and model organisms, such as Escherichia metabolic reconstructions (18, 20) is beyond
coli, Saccharomyces cerevisiae, Mus musculus, and the scope of the present review, an example
Arabidopsis thaliana, and are available through a of advanced computational methods illustrates

[Link] • Nutritional Metabolomics 193

 NU32CH10-Jones ARI 9 July 2012 19:2

the applicability for complex nutritional mod- Top-down nutritional metabolomics ap-
eling. Metabolic network reconstruction from proaches are analogous to a whole-body
genomic and gene expression data is composed physical examination in medicine; e.g., an
NMR: nuclear
magnetic resonance of a set of biochemical reactions and provides elevated blood low-density lipoprotein con-
insight into the hierarchical regulation of centration provides important information
PCA: principal
component analysis metabolic flux at a genome scale. However, en- about cardiovascular disease risk, but total
zyme activity and metabolomics data are needed cardiovascular disease risk is better evaluated
to provide information on metabolic flux. within the context of obesity, hypertension,
Yizhak et al. (104) used computational mod- exercise, and other risk factors. Although
eling to predict metabolic flux distribution for no ideal top-down nutritional metabolomics
genome-scale models by determining a steady- methods are currently available, important
state flux distribution in which flux through advances have been made with several analytic
reactions with measured proteomic and platforms. Proton nuclear magnetic resonance
metabolomic data is as consistent as possible (1 H-NMR) spectroscopy and phosphorous-31
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

with kinetically derived flux estimations. Such NMR (31 P-NMR) spectroscopy provide spec-
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approaches provide a foundation for nutritional tral measurements that are directly and quanti-
studies where high-throughput metabolomics tatively related to abundance of chemicals (12,
data are becoming available for nutritional 93). Many of the signals overlap and are difficult
deficiency and excess models. Although limited to relate unambiguously to individual chem-
high-throughput flux measurement capabil- icals, but the methods are useful to measure
ities exist, such modeling approaches can abundant chemicals, such as macronutrients
support understanding of complex nutritional in energy metabolism, including fatty acids,
interactions at the level of an entire organism. sugars, and some amino acids (68). Inouye et al.
(42) used 1 H-NMR metabolomic data along
with transcriptomic and genomic variation to
show concurrent association of metabolites,
Top-Down Approaches Complement inflammation, and adiposity. Importantly,
Bottom-Up Metabolomics gene coexpression in circulating leukocytes was
With time, such approaches will yield an under- dependent upon plasma metabolites, showing
standing of responses of mammals to changes networks linkage with lipoproteins, lipids,
in the endogenous microbiome. At present, and amino acids. Stringer et al. (87) showed
however, the variability of the microbiome that quantitative metabolomics was potentially
introduces a complication in mammalian nutri- useful in sepsis-induced acute lung injury, and
tion that is difficult to address using a bottom- Park et al. (70) showed a progressive trajectory
up approach to nutrition at a personalized level. of the principal component analysis (PCA)
Each microorganism has a metabolome, and of plasma metabolites in albumin-treated
the metabolomes of these organisms interact patients toward a normal healthy metabolic
with each other as well as with the host mam- profile. The most discriminatory regions by
malian metabolome. Thus, even though rapid PCA consisted of parts of the spectra in which
progress is currently being made to understand amino acids, glucose, and other metabolites
normative characteristics of the human and are present, suggesting utility to evaluate
mouse microbiomes, individual nutritional nutritional imbalance of critical illness and to
modeling becomes unwieldy without a priori assess recovery from critical illness (70).
knowledge of the contributions of thousands of Tracer methods using carbon-13 NMR
microbial species within an individual. For such (13 C-NMR) spectroscopy also provide the
purposes, top-down nutritional metabolomics ability to measure flux in pathways containing
approaches provide a critical complement to high-abundance metabolites, such as metabolic
the bottom-up computational frameworks. interactions of pathogenic and commensal

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bacteria (66). Analogous magnetic resonance are widely available to characterize metabolic
spectroscopy (MRS) methods measure metabo- patterns associated with nutritional variables
lites in vivo, and such studies were used many and other data-analytic needs in nutritional
FDR: false discovery
years ago to study nutrient effects on muscle metabolomics research (79). Clustering al- rate
energy metabolism (2) and more recently to gorithms to simplify complexity or select a
show that three days of a sulfur amino acid–free smaller subset of chemicals or subpopulations
diet has no detectable effect on brain GSH but for targeted investigation are widely available
increases midbrain glutamate and has effects on in biostatistical software packages; hierarchical
other high-abundance metabolites in humans cluster analysis (HCA) is commonly used in nu-
(74). trition research in gene expression analysis and
High-resolution mass spectrometry meth- can similarly be used to subgroup metabolites or
ods provide capabilities for comprehensive top- individuals according to metabolic character-
down analysis by supporting measurement of istics without a priori knowledge of metabolic
thousands of metabolites, with relatively high pathways or health phenotype. PCA and partial
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

throughput and minimal sample processing. least squares are also widely available to reduce
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Associated limitations are the capability to sup- complexity by extracting information on factors
port only relative quantification of most species contributing to differences among the samples.
and the inclusion of large numbers of uniden- Both HCA and PCA are also widely considered
tified chemicals. Moreover, statistical meth- unbiased in the sense that they classify samples
ods must be applied with caution because of without assignment of identifiers to the sam-
the large number of comparisons in associated ples. However, both can be biased in complex
datasets. Methods based upon the principles biosystems analyses because analytic meth-
of false discovery rate (FDR) (5), and positive ods can omit lower-abundance metabolites.
FDR (86), are valuable for analysis, but these Furthermore, higher-abundance metabolites
methods are limited in that metabolic adapta- often contribute more to the total variance
tion can result in an appearance of no effect so that mean-centering and autoscaling of
when substantial pathway effects are present. abundance data can be important to evaluate
For instance, proteolysis and gluconeogene- metabolomic profiles in an unbiased manner. A
sis maintain blood amino acid and glucose limit to this approach is that lower-abundance
concentrations during starvation, with some, chemicals often have greater analytical variabil-
but not all, related metabolites significantly al- ity, so scaling and normalization procedures
tered (21, 38). Consequently, for nutritional commonly used in statistics can introduce
metabolomics, there remains a need for robust bias in bioinformatics. Critical reviews and
statistical methods to complement those for in- commentaries on sample collection, metabolic
dividual metabolites and test for pathway and profiling, and data analysis provide impor-
network effects involving multiple metabolites. tant progress in nutritional metabolomics
(79).
Advances in probability-based clustering
Bioinformatics for Top-Down (85) allow coregulated metabolites to be iden-
Metabolomics tified, moving forward capabilities for delin-
Common approaches for top-down nutri- eation of the hierarchical structure of metabolic
tional metabolomics rely upon bioinformatics organization. Such approaches are not always
methods, which include both statistical and reliable because genes of the same pathway can
nonstatistical methods. The broader approach be regulated very differently (92). Nonetheless,
of chemometrics, developed over several advances in these methods enable subclassifica-
decades (7), uses multivariate statistics, applied tion of the pan-metabolome based upon associ-
mathematics, and computer science to address ations of unidentified metabolites with known
chemistry, biology, and medicine. Methods metabolites and metabolic pathways (84). In

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the context of carefully designed nutritional means to monitor clinically relevant responses
intervention studies, such data will support to specific nutritional interventions.
genome-scale nutritional metabolomics models
Fractal analysis: an
approach to quantify as needed for personalized nutrition. Toward
this goal, important advances have been made CONCLUSIONS AND NEW
the regularity in
behavior of a in standardization of metabolomics data to sup- PERSPECTIVES
characteristic of a port nutrition research (78), but cumulative Nutrition sciences have a rich tradition of
biologic system as a
databases of quantitative human metabolomics dealing with food and nutrient requirements
means to discriminate
unhealthy (more data are not yet well developed or widely for heterogeneous populations, simplifying the
regular) and healthy available. inherent complexity into manageable recom-
(more irregular) mendations in the form of dietary guidance for
individuals the purpose of avoiding disease. Although this
Artificial Intelligence: Fractal Analysis approach uses rigorous experimental designs
Artificial intelligence methods have been and sophisticated analytic and biostatistical
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

applied to nutritional metabolomics and may methods, it has inherent limitations due to
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be particularly useful to quantify metabolic assumptions that metabolic organizational

adaptability. An example is the use of fractal structure is uniform among individuals and
dynamics to measure irregularity and unpre- that direct cause-effect relationships exist. In
dictability in biological systems, as introduced addressing this complexity, Ziesel et al. (107)
by Goldberger (31). Fractal analysis shows introduced the concept that nutritional phe-
that irregularities of serial physiologic data are notype could be defined as an integrated set of
important features of health and adaptation; in genetic, proteomic, metabolomic, functional,
contrast, characteristics of disease are associ- and behavioral factors that, when measured,
ated with greater regularity of such data. This could provide the basis for assessment of human
is illustrated by fractal analysis of the human nutritional status. The nutritional phenotype
heartbeat, where a higher Hurst exponent (H), was proposed as a means to integrate the
indicative of greater heartbeat regularity, was effects of diet on disease/wellness and provide
associated with cardiovascular disease, while a a quantitative indication of the paths by which
more irregular heartbeat pattern, with a lower genes and environment exert their effects
H value, was observed in healthy individuals as on health. As summarized here, advances in
an indicator of greater adaptability to ambient available technologies and databases support
conditions (31, 32). Although not developed the use of nutritional metabolomics as a central
for nutritional assessment, fractal analysis component to define and measure the nutri-
of diurnal metabolic variation using wavelet- tional phenotype, initially across populations
transformed 1 H NMR spectra of human plasma with various states of health and disease, and
showed that H was predictive of the plasma ultimately at the level of individuals.
concentration of cysteine (47). More powerful Several key advances have been made to
multifractal approaches are also available to transition from cross-sectional descriptions of
improve description of metabolic regular- populations to useful models that are relevant
ity/irregularity by decomposing data into for individuals. Complex biosystems models
subsets characterized by multifractal spectra must accommodate single or multiple nutri-
with Holder exponent values that quantify local tional deficiencies and/or excesses as having dif-
behaviors, i.e., subregions of higher regularity ferent health phenotypic consequences among
and irregularity (43). Application of such meth- individuals, as well as different nutritional
ods to information-rich datasets could be useful variations among individuals contributing to
to detect metabolic consequences of subopti- common health phenotypes. Such charac-
mal nutrition that may warrant more detailed teristics cannot be reliably predicted from
clinical follow-up or to provide quantitative normative responses with single cause-effect

196 Jones · ·
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 NU32CH10-Jones ARI 9 July 2012 19:2

relationships. Advances that enable use of from pharmaceutics, commercial products,

nutritional metabolomics to support complex and other environmental exposures (Figure 1).
biosystems models include the delineation of a Rapid adaptation of chemometric methods to
conceptual grid for the exposome, a transition nutritional metabolomics and evolution of new
from disease-oriented to health-oriented bioinformatic and computational methods, as
nutrition, and a transition from a reductionist well as artificial intelligence, have set the stage
approach to one that incorporates nonreduc- to focus nutrition research on requirements of
tionist complex biosystems approaches. These complex biosystems within individuals. These
conceptual advances are enhanced by improved advances in nutritional metabolomics portend
analytic techniques allowing relative quantifica- a major shift in nutritional assessment and
tion of thousands of metabolites, encompassing intervention from those based upon normative
the core nutritional metabolome, the broader characteristics of populations to ones utilizing
food metabolome, a microbiome-associated complex biosystems approaches that may
metabolome, and a range of chemicals derived better account for individual nutritional needs.
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]
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SUMMARY POINTS
1. Available technologies and databases support the use of nutritional metabolomics as a
central component to define and measure the nutritional phenotype.
2. The nutritional metabolome is a critical component of the conceptual grid of the expo-
some, i.e., incorporating nutrition exposures from conception onward.
3. Nutritional metabolomics is rapidly maturing as an experimental approach in the field
of nutrition science to support integration of diet and nutrition in complex biosystems
research.
4. Personalized computational models can be developed to use nutritional metabolomics
to forecast health risks and treatment outcomes, thereby facilitating the transition from
population-based to individual-based nutrition.
5. High-resolution mass spectrometry provides sufficient sensitivity and metabolic coverage
to support metabolome-wide association studies of nutrition and disease.
6. An array of chemical and metabolic databases, bioinformatic methods, and computational
approaches is available to enhance the use of metabolomics in nutrition research.

FUTURE ISSUES
1. Systematic application of metabolomics to life-cycle nutrition research provides a logical,
central foundation for the elaboration of the conceptual grid of the exposome.
2. Mechanistic information is available to use with nutritional metabolomics data to support
the design and development of integrated systems models for nutrition health prediction.
3. Reference high-performance metabolic profiles and associated health outcomes data will
be needed as a resource for nutrition scientists to provide real tests of computational
models.

[Link] • Nutritional Metabolomics 197

 NU32CH10-Jones ARI 9 July 2012 19:2

4. There is a need to expand nutritional metabolomics coverage for both targeted (e.g.,
identification of potential direct or surrogate biomarkers of health and disease) and un-
targeted (e.g., identification of products of the microbiome) analysis in nutrition science.

DISCLOSURE STATEMENT
The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS
The authors thank J.F. Gregory, E.O. Voit, Y.-M. Go, J.R. Roede, and Q.A. Soltow for helpful
comments during manuscript preparation. D.P.J. is a Professor of Medicine supported in part by
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

NIH grants ES009047, ES011195, AG038746, NR012021, AA013757, ES016731, DK069322,

Access provided by Fudan University on 12/13/16. For personal use only.

and DK089369. Y.P. is an Assistant Professor of Medicine supported in part by NIH grants
AG038746, ES016731, DK089369, RR023356, and the Children’s Healthcare of Atlanta Center
for Developmental Lung Biology. T.R.Z. is a Professor of Medicine supported in part by NIH
grants DK069322, DK089369, HL110044, RR023356, and RR025008 and the Emory Global
Health Institute.

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a
Pan-metabolome

Core nutritional metabolome

Food Metabolome-wide
metabolome association studies
Nonnutritive chemicals in diet

Microbiome-related chemicals
Gene X metabolome
Supplements and pharmaceuticals
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

Commercial products
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Environmental Epigenome X metabolome

metabolome
Environmental chemicals

b Aging pan-metabolome

Adult pan-metabolome
ures
ex pos
long Adolescent and pubertal pan-metabolome
Life
Early development pan-metabolome

Fetal pan-metabolome

Early embryogenesis pan-metabolome

Maternal and paternal pan-metabolome Dietary nutrients and endogenous metabolites

Dietary nutrients andNon-nut

endogenous
Non-nutr
riti b lis in diet
itivve chemicals
ch
hemicals
hemical d

Dietary nutrients andNon-nut

endogenous
Non-nutr
riti hemibical
lisic
itivve chemicals
ch
hem ical cin
Microb
M iicr
ro
obdi
d
biome
biom e-related chemicals

Dietary nutrients andNon-nut

endogenous
Non-nutr
riti hemibical
lisic
itivve chemicals
ch
hem ical cin
Microb
M iicr
ro
obdi
d
biome
biom e-related
d chemicals
Supplemen
Suppleme nts and pharmaceuticals

Dietary nutrients andNon-nut

endogenous
Non-nutr
riti hemibical
hem lisic
itivve chemicals
ch ical cin
Microb
M iicr
ro
obdi
d
biome
biom e-related
d chemicals
Supplemen
Suppleme nts and ph
haCrom
omame
ceuticals
Commercial
m
merrcial p
pro
oducts

Dietary nutrients andNon-nut

endogenous
Non-nutr
riti hemibical
itivve ch
hem lisic
chemicals
ical cin
Microb
M iicr
ro
obdi
d
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biom e-related
d chemicals
Supplemen
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haCrom
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Commercial
m
merrcial p
pro
oductsEEn
nvironmental chemicals

Dietary nutrients andNon-nutritive

endogenous metabolites
chemicals
icrin diet e-related
Microbiome
M ic robiom d chemicals
Supplemen
Suppleme nts and ph
haCrom
omame
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Commercial
m
merrcial p
pro
oductsEEn
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Non-nutritive chemicals in diet

Microbiome-related
d chemicals
Supplemen
Suppleme nts and ph
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Commercial
m
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pro
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Supplements and pharmaceuticals

Commercial productsEEn
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Commercial productsEnvironmental chemicals

Environmental chemicals

[Link] • Nutritional Metabolomics C-1

 NU32CH10-Jones ARI 9 July 2012 19:2

←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
Figure 1
The nutritional metabolome as a component of the exposome. (a) The summation of all chemicals found
in an organism can be considered a “pan-metabolome.” Although no method is available to measure all
chemicals, the pan-metabolome can be conceptualized to contain a core nutritional metabolome derived
from required nutrients and related biochemicals derived from these nutrients in reactions catalyzed by
enzymes encoded in the organism. The food metabolome contains many components of this core nutritional
metabolome and also a large number of other nonnutritive chemicals. The pan-metabolome also contains
microbiome-related chemicals derived from food metabolites, drugs, and other environmental agents acted
upon by the intestinal microbes. Other components of the pan-metabolome are derived from dietary
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

supplements and pharmaceuticals, commercial products such as sunscreen and face creams, and
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environmental chemicals. (b) The exposome is defined as the cumulative exposures from conception onward.
Life-cycle nutritional requirements can be viewed within the conceptual grid of the exposome, including the
core nutritional metabolome and food metabolome as in panel a. Together, panels a and b provide a
conceptual grid for the exposome. Consequently, nutritional metabolomics represents a central and critical
component of exposome research, impacting expression of the genome and modification of the epigenome
through the life cycle.

−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−→
Figure 2
Nutritional metabolomics to support personalized nutrition. (a) Contemporary nutritional
recommendations and interventions use a normative approach based upon the characteristics of a healthy
population. Hypotheses are based upon experimental and epidemiologic studies and tested in clinical trials to
determine outcomes in individuals meeting certain phenotypic or nutritional criteria. Importantly, the
criteria are based upon population-based norms. A person with a predefined deviation from the norm is
prescribed an intervention based upon clinical trials that show that this intervention has a significant
beneficial effect in at least some of the individuals in the trial. Although cost-effective for the population, the
approach does not work for all individuals. (b) An integrated biosystems approach utilizes the hypotheses of
panel a along with information-rich nutritional metabolomics (systems data) for humans and model
organisms to develop computational models. The computational models are tested and refined to correctly
describe responses to differences in diet, genetics, or other factors. The computational models are used with
nutritional metabolomics data for an individual to provide personal health models for health prediction, risk
profiling, and treatments. The approach takes advantage of the knowledge base as in panel a but refines this
for personalized use. (c) An artificial intelligence approach can take advantage of nutritional metabolomics
(systems data) as in panel b but does not require mechanistic development. In this case, artificial intelligence
approaches are used to compare personal profiles to profiles and outcomes within a reference population to
obtain the best matches for prediction. This has advantages that there is no delay in building models, and the
power increases with the size of the reference population. On the other hand, due to the correlative nature of
these statistical models, there is no scientific foundation to facilitate development of new interventional
strategies. Based upon Reference 90.

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 NU32CH10-Jones ARI 9 July 2012 19:2

a Normative approach b Integrated biosystems c Artificial intelligence

approach approach

Epidemiology, Molecular Epidemiology, Molecular Extensive Detailed

disease outcomes studies disease outcomes studies reference outcomes
population data
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

systems data
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Population
Hypothesized Integrated systems data
biomarker-disease system model
associations design
Model organism
systems data Cumulative Personal
association systems data
matrix

Computational Personal
Clinical trials to model systems data
test biomarker- Personal
disease biomarker
associations, data Best match
outcomes Personal computational
health model algorithms

Health Risk Personal Health Risk Personal

prediction profile treatment prediction profile treatment

Prevention Treatment
plans based based upon Personal Personal
upon normative normative prevention prevention
distribution response plans plans

Advantages Advantages Advantages

Is cost-effective for a Predictions based upon Mechanistic understanding
population individual characteristics; not required; power increases
has scientific foundation with database size
Disadvantages Disadvantages Disadvantages
Does not work effectively for Multiple models possible; may Requires extensive reference
everyone within a population require lengthy development data; no scientific foundation

[Link] • Nutritional Metabolomics C-3

 NU32CH10-Jones ARI 9 July 2012 19:2

NAD + NAD

Mal OAA + Glu

Mitochondrial matrix
Asp + aKG

SLC25A13

Metabolic pathways
in cytoplasm
Xanthosine
Xanthosine
OMP
Choline
Choline Xanthine
Xanthine
Glycerol
Glycerol Phe Tyr
His Trp
Ser
Dimethylglycine
Gly Dimethylglycine
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

Val Arg
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Pyr Mal Lys

Pro Leu
Ala NADH Met
Glycocholate
Glycocholate
Glu

SLC6A12 System L System A

Plasma Phe Hcys

metabolites Pro Gly Met Ser
Leu Citr
β-alanine Choline His Asn

Diaminobutyrate Putrescine Ile Trp Lys Arg

Dimethylglycine Met Val Tyr

Figure 3
Development of multidimensional models for nutritional metabolomics. The recent use of unbiased pathway
models (15) has revealed an important multidimensional character to nutritional metabolomics. Differences
in plasma metabolite profiles in individuals with impaired glucose tolerance and normal glucose tolerance
were associated with transporters functioning in mitochondrial/cytoplasmic balance of nicotinamide adenine
dinucleotide (NAD+ ) and NADH (SLC25A13) and with cell membrane transporters involved in amino acid
transport (system A and system L) and osmotic regulation (SLC6A12). In this schematic representation
based upon the Kyoto Encyclopedia of Genes and Genomes (KEGG) human metabolic pathway map, the
plasma metabolome (bottom) is linked to KEGG biochemical pathways in the cytoplasm (middle) through
system A, system L, and SLC6A12, and a subset of metabolites in the cytoplasm is linked to the
mitochondrial matrix through the glutamate-aspartate transporter (SLC25A13). Some metabolites are not
labeled due to lack of space. Based upon findings of Reference 15.

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Mass spectrometry–based profiling approaches for chemicals with similar mass

C24H36O5 + C25H40O4
(m/z 404.256) (m/z 404.293)

a LC-MS or GC-MS b LC-MS/MS c High-resolution MS

Requires separation of same Measures based upon Minimizes separation or
nominal mass prior to MS fragmentation pattern; less fragmentation needs;
separation requirement often can predict
elemental composition

100 100 100

90 m/z 404.3 90 m/z 404.3 90
Relative abundance

Relative abundance

Relative abundance
80 80 80 m/z 404.256
70 70 70
60 60 60
50 50 50
40 40 40 C24H36O5
30 30 30
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

20 20 20
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10 10 10
0 0 0
Retention time Retention time Retention time

100 100 Product 100

90 m/z m/z 90 ions 90
Relative abundance

Relative abundance

Relative abundance
80 404.3 404.3 80 80 m/z 404.293
70 70 70
60 60 60
50 50 50
40 40 40 C25H40O4
30 30 30
20 20 20
10 10 10
0 0 0
Retention time m/z Retention time

Figure 4
Comparison of mass spectrometry (MS)-based metabolic profiling approaches for chemicals that have similar
but not identical mass. (a) Analysis with gas chromatography (GC) or liquid chromatography (LC) with a
single low-resolution mass detector requires separation of chemicals prior to detection. (b) Analysis with a
tandem mass spectrometer using either GC or LC often does not require complete separation because ion
dissociation and detection of product ions support identification without separation. However, quantification
typically requires a stable isotopic form of chemicals of interest for internal standardization. (c) LC coupled
to high-resolution mass spectrometry supports high-throughput analysis because chemicals are resolved by
mass and have less demand for chromatographic separation. High-resolution instruments include
Fourier-transform ion cyclotron resonance, Orbitrap (Thermo), and newer time-of-flight instruments (62).

[Link] • Nutritional Metabolomics C-5

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Glycan Lipid Carbohydrate Amino acid Nucleotide Cofactor

metabolism metabolism metabolism metabolism metabolism metabolism
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Xenobiotic Terpenoid Energy Other secondary Other amino acid
metabolism metabolism metabolism metabolism metabolism

Figure 5
Intermediary metabolites detected in 10-minute liquid chromatography–Fourier transform mass spectrometry (LC-FTMS) analysis of human plasma. Matches for ions
detected by LC-FTMS with high-resolution mass/charge (m/z) in human plasma to metabolites in the Kyoto Encyclopedia of Genes and Genomes (KEGG) human
metabolic pathways. MS data were extracted using adaptive processing of high-resolution liquid chromatography/mass spectrometry data (105). Larger dots represent
matches for 745 metabolites found in plasma from human, rhesus macaque, common marmoset, rat, mouse, pig, and sheep. Metabolites are present for 136 out of 154
pathways in the database. Figure based upon results of Reference 73.
 NU32-FrontMatter ARI 26 June 2012 13:26

Annual Review of
Nutrition
Contents Volume 32, 2012

An Unexpected Life in Nutrition

Malden C. Nesheim p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1
Endoplasmic Reticulum Stress in Nonalcoholic Fatty Liver Disease
Michael J. Pagliassotti p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p17
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]

Modeling Metabolic Adaptations and Energy Regulation in Humans

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Kevin D. Hall p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p35

Hypomagnesemia and Inflammation: Clinical and Basic Aspects
William B. Weglicki p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p55
Selenoproteins and Cancer Prevention
Cindy D. Davis, Petra A. Tsuji, and John A. Milner p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p73
The Role of Vitamin D in Pregnancy and Lactation:
Insights from Animal Models and Clinical Studies
Christopher S. Kovacs p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p97
Vitamin A Metabolism in Rod and Cone Visual Cycles
John C. Saari p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 125
Lipoprotein Lipase in the Brain and Nervous System
Hong Wang and Robert H. Eckel p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 147
New Roles of HDL in Inflammation and Hematopoiesis
Xuewei Zhu and John S. Parks p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 161
Nutritional Metabolomics: Progress in Addressing Complexity
in Diet and Health
Dean P. Jones, Youngja Park, and Thomas R. Ziegler p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 183
Resolvins: Anti-Inflammatory and Proresolving Mediators Derived
from Omega-3 Polyunsaturated Fatty Acids
Michael J. Zhang and Matthew Spite p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 203
Visfatin/NAMPT: A Multifaceted Molecule with Diverse Roles
in Physiology and Pathophysiology
Tuva B. Dahl, Sverre Holm, Pål Aukrust, and Bente Halvorsen p p p p p p p p p p p p p p p p p p p p p p p 229
Gene-Environment Interactions in the Development of Type 2
Diabetes: Recent Progress and Continuing Challenges
Marilyn C. Cornelis and Frank B. Hu p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 245

v
 NU32-FrontMatter ARI 26 June 2012 13:26

Mechanisms of Inflammatory Responses in Obese Adipose Tissue

Shengyi Sun, Yewei Ji, Sander Kersten, and Ling Qi p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 261
Bone Metabolism in Obesity and Weight Loss
Sue A. Shapses and Deeptha Sukumar p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 287
Obesity in Cancer Survival
Niyati Parekh, Urmila Chandran, and Elisa V. Bandera p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 311
Inflammation in Alcoholic Liver Disease
H. Joe Wang, Bin Gao, Samir Zakhari, and Laura E. Nagy p p p p p p p p p p p p p p p p p p p p p p p p p p p 343
Lessons Learned from Randomized Clinical Trials of Micronutrient
Supplementation for Cancer Prevention
Susan T. Mayne, Leah M. Ferrucci, and Brenda Cartmel p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 369
Annu. Rev. Nutr. 2012.32:183-202. Downloaded from [Link]
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Population-Level Intervention Strategies and Examples for Obesity

Prevention in Children
Jennifer L. Foltz, Ashleigh L. May, Brook Belay, Allison J. Nihiser,
Carrie A. Dooyema, and Heidi M. Blanck p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 391
Type 2 Diabetes in Asians: Prevalence, Risk Factors, and Effectiveness
of Behavioral Intervention at Individual and Population Levels
Mary Beth Weber, Reena Oza-Frank, Lisa R. Staimez, Mohammed K. Ali,
and K.M. Venkat Narayan p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 417

Indexes

Cumulative Index of Contributing Authors, Volumes 28–32 p p p p p p p p p p p p p p p p p p p p p p p p p p p 441

Cumulative Index of Chapter Titles, Volumes 28–32 p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 444

Errata

An online log of corrections to Annual Review of Nutrition articles may be found at

[Link]

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